Transcoding video that is a 2 in 1

[llebeloc]

I have a video file that has the theatrical and alternate version. So my question is how i transcode the file? I know how to do it with multiavchd but what settings do i use under directvob as when i right click it it shows

Show subtitles or hide subtitles
It has both version of the subtitles for both versions
And it has the source for either theatrical or alternate version

Which one do i check? Do i just check hide subtitles so they wont be hardcoded? As i want to have the option to turn them on if i want when watching the dvd...

Thanks in advance and sorry if this is the wrong section to post this.

[llebeloc]

Ive tried it with a sample and just left everything the way it was and after transcoding it went to encode the subtitles and said it may take awhile and after five minutes the program gave a error and shutdown by itself...

Is it better to use uncropmkv as the video isnt compliant which is the reason why i encoded it in the first place and just take out the subtitles? And since the file is about 7gb can i under bitrate suggestions choose to have it on a single dvd5 or does it have to be on a dvd9?

Thx again and sorry for all the questions i pretty much figured everything else out except this